def install_db_patches():
with prefix(env.activate):
with prefix(env.proj_pythonpath):
with show('stdout'):
print green("Installing db_patches")
src = os.path.join(env.proj_dir, 'src', 'install_db_patches.py')
run('python %s update' % src)
def package_update():
""" Update the environment using the package manager """
with prefix('source '+env.homedir+'/.bashrc'):
with prefix(env.activate):
with prefix('workon %s' % env.venv):
with cd('%s/APM/System/dvt/Tools/fortytwo/setup' % env.accurev.accurev_home):
sudoenv('pip install --requirement %s/APM/System/dvt/Tools/fortytwo/setup/fortytwo_pip_reqts.txt' % env.accurev.accurev_home)
def deploy_static_files():
sudo('mkdir -p /var/www/bongo/static/')
with cd(GIT_TOP_LEVEL):
with prefix('export HOME=/home/bongo'):
with prefix('source /usr/local/bin/virtualenvwrapper.sh'):
with prefix('workon bongo'):
sudo('./manage.py collectstatic -v0 --noinput', 'bongo')
def clear_databases():
""" Clear out all databases. This is very destructive, only useful for testing! """
require('hosts', provided_by=['dev', 'staging', 'production'])
ans = prompt('This will completely wipe out the database. Are you sure (YES/no)?')
if ans != 'YES':
print yellow('Glad you were just kidding.')
return
ans = prompt(yellow('%s' % env.hosts[0]) + ' database will be wiped. Are you sure (YES/no)?')
if ans != 'YES':
print "Didn't think so."
return
run('supervisorctl stop all')
print yellow('Recreate WEB database')
run('dropdb ocl_web')
run('createdb -O deploy ocl_web')
# setup DB
with prefix('source /opt/virtualenvs/ocl_web/bin/activate'):
with prefix('export DJANGO_CONFIGURATION="Production"'):
with prefix('export DJANGO_SECRET_KEY="blah"'):
print yellow('creating WEB database...')
run('/opt/deploy/ocl_web/ocl_web/manage.py syncdb --noinput --migrate')
print yellow('Recreate API database')
run('echo -e "use ocl \n db.dropDatabase();" | mongo')
create_api_database()
def _install_requirements(self):
# needed for private repos, local keys get forwarded
env.forward_agent = True
env.user = config['USER']
env.remote_home = "/home/" + config['USER']
virtualenv_dir = '%s/.virtualenvs/%s' % (env.remote_home, env.project_name)
info("DJANGO: install python modules in virtualenv %s" % virtualenv_dir)
# from requirements.txt
with prefix('. %s/bin/activate' % virtualenv_dir):
with cd("%s/code/%s" % (env.remote_home, env.project_name)):
cmd = "pip install " \
"--download-cache=/var/cache/pip " \
"-r requirements.txt"
debug("PIP: " + cmd)
out = self.execute(run, cmd)
for host, value in out.iteritems():
debug(value, host=host)
# from class variable
if hasattr(self.__class__, "python_packages"):
for package in self.__class__.python_packages.split(" "):
with prefix('. %s/.virtualenvs/%s/bin/activate' % (env.remote_home, env.project_name)):
with cd("%s/code/%s" % (env.remote_home, env.project_name)):
out = self.execute(run, "pip install --download-cache=/var/cache/pip %s"
% (package))
for host, value in out.iteritems():
debug(value, host=host)
def get_platform(self):
# Be sure we don't get stuck in a virtualenv for free.
with prefix('deactivate >/dev/null 2>&1 || true'):
out = run("python -c 'import lsb_release; "
"print lsb_release.get_lsb_information()'",
quiet=not DEBUG, combine_stderr=False)
try:
self.lsb = SimpleObject(from_dict=ast.literal_eval(out))
self.is_osx = False
except SyntaxError:
self.lsb = None
self.is_osx = True
# Be sure we don't get stuck in a virtualenv for free.
with prefix('deactivate >/dev/null 2>&1 || true'):
out = run("python -c 'import platform; "
"print platform.mac_ver()'", quiet=not DEBUG,
combine_stderr=False)
try:
self.mac = SimpleObject(from_dict=dict(zip(
('release', 'version', 'machine'),
ast.literal_eval(out))))
except SyntaxError:
# something went very wrong,
# none of the detection methods worked.
raise RuntimeError(
'cannot determine platform of {0}'.format(self.host_string))
def _update_virtualenv(source_folder):
with prefix('export WORKON_HOME=$HOME/.virtualenvs'):
with prefix('export PROJECT_HOME=$HOME/sites'):
with prefix('export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3'):
with prefix('source /usr/local/bin/virtualenvwrapper.sh'):
with prefix('workon tdd'):
run('pip install -r %s/requirements.txt' % (source_folder,))
def rebuild_index():
""" Rebuild search index """
with prefix("source /opt/virtualenvs/ocl_api/bin/activate"):
with prefix('export DJANGO_CONFIGURATION="Production"'):
sudo('/etc/init.d/jetty restart')
sleep(5)
run("/opt/deploy/ocl_api/ocl/manage.py rebuild_index")
def bash_profile():
"""
Fixes stuff that non-interactive shells don't do automatically.
"""
with prefix('export HOME={}'.format(project_home())), \
prefix('source {}/.bash_profile'.format(project_home())):
yield
def push_code():
require('hosts')
require('code_root')
import time
env.release = time.strftime('%Y%m%d%H%M%S')
tar_file = '%s.tar.gz' % (env.release,)
local('git archive --format=tar master | gzip > %s' % (tar_file,))
put(tar_file, '%s/packages/' % env.code_root)
run('mkdir -p %s/releases/%s/pywars' % (env.code_root, env.release))
run('cd %s/releases && tar zxf ../packages/%s.tar.gz -C %s/releases/%s/pywars' % (env.code_root, env.release, env.code_root, env.release))
with prefix('source %s/bin/activate' % (env.code_root,)):
run("cd %s/releases/%s/pywars; pip install -r requirements.txt" % (env.code_root, env.release))
run('cd %s/releases/%s/pywars; pip install mysql-python')
run('cd %s/releases/%s/pywars; python manage.py bower install' % (env.code_root, env.release))
run("cd %s/releases/%s/pywars; python manage.py collectstatic --noinput" % (env.code_root, env.release))
local('rm -fr %s' % (env.release,))
local('rm %s' % (tar_file,))
symlink_current_release()
with settings(warn_only=True):
# copy the local_settings for deployment
run("cp /home/%s/local_settings.py %s/releases/%s/pywars/battleground/" % (env.user, env.code_root, env.release))
with prefix('source %s/bin/activate' % (env.code_root,)):
run("cd %s/releases/%s/pywars; python manage.py migrate" % (env.code_root, env.release))
def conf(mode=None):
"""Switch Refinery configurations on Vagrant VM"""
if (mode is None) or (env.hosts != ['[email protected]:2222']):
abort("usage: fab vm conf:<mode>")
modes = ['dev', 'djdt', 'gdev', 'prod']
if mode not in modes:
abort("Mode must be one of {}".format(modes))
puts("Switching Refinery running on Vagrant VM to '{}' mode".format(mode))
env.shell_before = "export DJANGO_SETTINGS_MODULE=config.settings.*"
env.shell_after = \
"export DJANGO_SETTINGS_MODULE=config.settings.{}".format(mode)
env.apache_before = "SetEnv DJANGO_SETTINGS_MODULE config.settings.*"
env.apache_after = \
"SetEnv DJANGO_SETTINGS_MODULE config.settings.{}".format(mode)
# stop supervisord and Apache
with prefix("workon {refinery_virtualenv_name}".format(**env)):
run("supervisorctl shutdown")
sudo("/usr/sbin/service apache2 stop")
# update DJANGO_SETTINGS_MODULE
sed('/home/vagrant/.profile', before=env.shell_before,
after=env.shell_after, backup='')
sed('/etc/apache2/sites-available/001-refinery.conf',
before=env.apache_before, after=env.apache_after, use_sudo=True,
backup='')
# update static files
with cd(env.refinery_ui_dir):
run("grunt make")
with prefix("workon {refinery_virtualenv_name}".format(**env)):
run("{refinery_app_dir}/manage.py collectstatic --clear --noinput"
.format(**env))
# start supervisord and Apache
with prefix("workon {refinery_virtualenv_name}".format(**env)):
run("supervisord")
sudo("/usr/sbin/service apache2 start")
def ring():
"""
Bootstrap Scality RING (environment variable `SCAL_PASS` must be exported).
The environment variable `SCAL_PASS` is expected to hold username:password
for fetching scality packages.
"""
install_env = {
'SUP_ADMIN_LOGIN': '******',
'SUP_ADMIN_PASS': '******',
'INTERNAL_MGMT_LOGIN': '******',
'INTERNAL_MGMT_PASS': '******',
'HOST_IP': env.host,
'SCAL_PASS': os.environ['SCAL_PASS'],
}
export_vars = ('{0:s}={1:s}'.format(k, v) for k, v in install_env.items())
export_cmd = 'export {0:s}'.format(' '.join(export_vars))
utils.apt_get(['git-core'])
run('git clone https://github.com/scality/openstack-ci-scripts.git')
# Hide aborts to not leak any repository passwords to console on failure.
with cd('openstack-ci-scripts/jenkins'), prefix(export_cmd):
with prefix('source ring-install.sh'), settings(hide('aborts')):
run('add_source')
run('install_base_scality_node', pty=False) # avoid setup screen
run('install_supervisor')
run('install_ringsh')
run('build_ring')
run('install_sproxyd')
run('test_sproxyd')
def config():
global repo_path
_printOut('Creating repo on: '+str(env.hosts))
with cd('/sites/'):
sudo('hg clone ssh://[email protected]/rccomunicacao/{{PROJECT_NAME}}', user='******')
with cd(repo_path):
sudo('virtualenv --distribute env', user='******')
with prefix('source env/bin/activate'):
print('Installing environment')
sudo('pip install -r requirements.txt', user='******')
sudo('cp {{PROJECT_ID}}/local_settings_template.py {{PROJECT_ID}}/local_settings.py', user='******')
database_name = prompt('Name of MySQL database to be created: ', default='{{PROJECT_ID}}')
sudo('mysql -u root -p -e "create database %s"'%database_name, user='******')
print('Now starting the configure of the local_settings.py module')
config_local_settings()
put('{{PROJECT_ID}}/server_local_settings.py', '{{PROJECT_ID}}/local_settings.py', use_sudo=True)
sudo('chown www-data:www-data {{PROJECT_ID}}/local_settings.py')
with prefix('source env/bin/activate'):
sudo('python manage.py syncdb', user='******')
print('Configure wsgi bridge file')
config_wsgi_file()
sudo('mkdir apache', user='******')
put('apache_wsgi.wsgi', 'apache/django.wsgi', use_sudo=True)
sudo('chown www-data:www-data apache/django.wsgi')
sudo('/etc/init.d/apache2 reload')
def django(path_=path('web')):
return nested(
cd(path_),
prefix('export DJANGO_SETTINGS_MODULE=goma.settings.' + env.environment),
prefix('source ' + path('secret', 'env')),
prefix('source ' + path('venv', 'goma', 'bin', 'activate')),
)
def bootstrap(cloud_config_file_name):
"""Edit the test client props file (under resources) according to your client machine, prepare your cloud config
file, put it under resources and pass it as cloud_config_file_name"""
run('sudo apt-get update')
run('sudo apt-get -y install python-pip')
run('sudo apt-get -y install git')
run('sudo pip install virtualenv')
run('virtualenv ' + env_name)
with prefix('source ' + env_name + '/bin/activate'):
run('pip install --process-dependency https://github.com/CloudifySource/cosmo-cli/archive/develop.zip')
run('sudo apt-get -y install python-dev')
run('pip install https://github.com/CloudifySource/cloudify-openstack/archive/develop.zip')
run('mkdir ' + work_dir_name)
with prefix('source ../' + env_name + '/bin/activate'):
with cd(work_dir_name):
run('cfy init openstack')
run('mv cloudify-config.yaml cloudify-config.yaml.backup')
put('../resources/' + cloud_config_file_name, work_dir_name)
with cd(work_dir_name):
run('mv ' + cloud_config_file_name + ' cloudify-config.yaml')
with prefix('source ../' + env_name + '/bin/activate'):
with cd(work_dir_name):
run('cfy bootstrap -a -v')
def _update_database(source_folder):
with prefix('export WORKON_HOME=$HOME/.virtualenvs'):
with prefix('export PROJECT_HOME=$HOME/sites'):
with prefix('export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3'):
with prefix('source /usr/local/bin/virtualenvwrapper.sh'):
with prefix('workon tdd'):
run('cd %s && python3 manage.py migrate --noinput' % (source_folder,))
def fix_solr():
""" Fix solr
work in progress
"""
with cd('/var/tmp'):
print blue('pulling new code...')
sudo('/etc/init.d/jetty stop')
sleep(5)
# run('rm -rf /opt/deploy/solr/collection1')
print blue('copying new code...')
# run('mkdir -p /opt/deploy/solr/collection1')
# run("cp -r oclapi/solr/collection1/conf /opt/deploy/solr/collection1")
with cd("/opt/deploy/ocl_api/ocl"):
# there is no need for this, settings.py.eploy is actually wrong?
# run("cp settings.py.deploy settings.py")
with prefix('source /opt/virtualenvs/ocl_api/bin/activate'):
with prefix('export DJANGO_CONFIGURATION="Production"'):
with prefix('export DJANGO_SECRET_KEY="blah"'):
# this is really slow because it pull down django-norel
run('./manage.py build_solr_schema > ' +
'/opt/deploy/solr/collection1/conf/schema.xml')
sleep(5)
sudo('/etc/init.d/jetty start')
def remove(project_name, db_password=""):
"""
Remove an existing project on your computer.
WARNING: This script will not back up your source code before deletion.
Usage:
remove:<project_name>
remove:<project_name>,<db_password>
"""
# check for the database
if not testdb(db_password):
return
with prefix("source ~/%s" % env.bash_profile):
# check to see if the virtual env has been fully removed, not removed because of compiled stuff
bash_local("rmvirtualenv %s" % project_name)
workon_home = os.getenv('WORKON_HOME')
if exists("%s/%s" % (workon_home, project_name)):
bash_local("sudo rm -rf %s/%s" % (workon_home, project_name))
# remove the source code directory
if exists("%s/%s/.git" % (project_name, project_name)):
question = prompt("Do you want to remove the local copy of `%s` (Y/[N])?" % project_name,validate="^[YyNn]?$")
if not (question == 'y' or question == 'Y'):
return
bash_local("rm -rf %s/%s/.git" % (project_name,project_name))
bash_local("rm -r %s" % project_name)
elif exists("%s/.git" % project_name):
question = prompt("Do you want to remove the local copy of `%s` (Y/[N])?" % project_name,validate="^[YyNn]?$")
if not (question == 'y' or question == 'Y'):
return
bash_local("rm -rf %s/.git" % project_name)
bash_local("rm -r %s" % project_name)
elif exists("%s" % project_name):
question = prompt("Do you want to remove the only copy of `%s` from your computer (Y/[N])?" % project_name,validate="^[YyNn]?$")
if not (question == 'y' or question == 'Y'):
return
bash_local("rm -r %s" % project_name)
# don't remove the database but tell the user
if env.database == "mysql":
with prefix('export PATH="$PATH:/usr/local/mysql/bin/"'):
with settings(warn_only=True):
if len(db_password):
cmd = "mysql -u root --password=%s -e 'use %s'" % (db_password,project_name)
else:
cmd = "mysql -u root -e 'use %s'" % project_name
output = bash_local(cmd)
# don't actually remove the database for now
if output.succeeded:
print yellow("Your database still exists. You should remove it manually by calling\n fab removedb:%s,<db_password>" % project_name)
else:
print yellow("To remove the project's database:\n fab removedb:%s,<db_password>" % project_name)
def appserver_start():
""" Start the app server. Kill any instances of the appserver first. """
appserver_stop()
with prefix('source '+env.homedir+'/.bashrc'):
with prefix(env.activate):
with prefix('workon %s' % env.venv):
with cd('%s/APM/System/dvt/Tools/fortytwo' % env.accurev.accurev_home):
sudoenv('gunicorn sandbox.wsgi:application -c %s/gunicorn_%s.conf.py' % (env.confdir, env.venv))
def collectstatic():
"""
Collect the static files to the webserver's static directory
"""
with prefix('source '+env.homedir+'/.bashrc'):
with prefix(env.activate):
with prefix('workon %s' % env.venv):
with cd('%s/APM/System/dvt/Tools/fortytwo/sandbox' % env.accurev.accurev_home):
sudoenv('python ./manage.py collectstatic --noinput --clear --verbosity=0')
def inner(*args, **kwargs):
if venv_wrap:
with prefix('source /usr/local/bin/virtualenvwrapper.sh && workon {0}'.format(project_name)):
return func(*args, **kwargs)
if path is not None:
with prefix('source {0}'.format(activate)):
return func(*args, **kwargs)
else:
return func(*args, **kwargs)
def test_nested_prefix():
"""
prefix context managers can be created outside of the with block and nested
"""
cm1 = prefix('1')
cm2 = prefix('2')
with cm1:
with cm2:
eq_(env.command_prefixes, ['1', '2'])
def install(self):
for package in self.packages:
print(green('Installing %s via pip' % package))
with prepare_venv():
with prefix(self.workon_cmd):
if self.additionalcmd:
with prefix(self.additionalcmd):
run('pip install %s' % package)
else:
run('pip install %s' % package)
def requirements():
"""
:: Update Python dependencies on remote host.
"""
require('project', provided_by=('staging', 'production'))
with prefix("export PROJECT_HOME=%(projserver)s" %env):
with prefix("export WORKON_HOME=%(envserver)s" %env):
with prefix("source /usr/local/bin/virtualenvwrapper.sh"):
run("workon %(project)s; pip install -r %(requirements)s; deactivate" % env)
def load_site_name():
"""
Set the global site object value in the web server, used in outbound emails.
"""
with cd('/opt/deploy/ocl_web'):
with prefix('source /opt/virtualenvs/ocl_web/bin/activate'):
with prefix('export DJANGO_CONFIGURATION="Production"'):
with prefix('export DJANGO_SECRET_KEY="blah"'):
print yellow('setting site name...')
run('ocl_web/manage.py loaddata ocl_web/config/sites.%s.json' % env.site_spec)
def virtualenv():
"""
:: Setup virtualenv on remote host.
"""
require('project', provided_by=('staging', 'production'))
with prefix("export PROJECT_HOME=%(projserver)s" %env):
with prefix("export WORKON_HOME=%(envserver)s" %env):
with prefix("source /usr/local/bin/virtualenvwrapper.sh"):
run("mkproject %(project)s" % env)
def del_app():
"""
:: Delete project
"""
require('project', provided_by=('staging', 'production'))
with cd(env.projserver):
with prefix("export PROJECT_HOME=%(projserver)s" %env):
with prefix("export WORKON_HOME=%(envserver)s" %env):
with prefix("source /usr/local/bin/virtualenvwrapper.sh"):
run('rm -rf %(project)s; rmvirtualenv %(project)s' %env)
def deploy():
require('deployment_location', used_for=USED_FOR_MSG)
if hasattr(env, 'brand_path'):
with cd(env.brand_path), prefix('source %(sandbox_activate)s' % env):
run('git pull --rebase')
with cd(env.project_root), prefix('source %(sandbox_activate)s' % env):
run('git pull --rebase')
run('pip install -r requirements-dep.txt')
run('python manage.py alembic upgrade head')
run('supervisorctl -c %(supervisord_conf)s restart all' % env)
def install(self):
print(green('Installing %s packages' % self.repo_name))
for package in self.packages:
print(green('Installing %s package: %s' % (self.repo_name,
package)))
with prefix('export PATH=%s/bin:$PATH' % self.anaconda_path):
with prefix(self.workon_cmd):
with prefix("cd " + self.repo_path):
with prefix("cd " + package):
run('python setup.py develop')
print(green('%s Installation successfull' % self.repo_name))
def deploy():
build_assets()
local('git push')
with cd(env.directory):
run("git stash")
run("git pull")
with prefix(env.activate):
with prefix(env.additional_env):
run("pip install -r requirements.txt")
run("python manage.py db upgrade")
run("touch django_wsgi.py")
def umask(value='002'):
return prefix('umask {value}'.format(value=value))
def init():
"""Initialize the website"""
with prefix(env.workon):
run("./biostar.sh init")
def stats():
code_dir = '/home/b402/beta402'
with cd(code_dir), prefix('source ve/bin/activate'):
run('./manage.py stats')
def light_deploy():
code_dir = '/home/b402/beta402'
with cd(code_dir), prefix('source ve/bin/activate'):
run('sudo supervisorctl stop b402-gunicorn')
run("git pull")
run('sudo supervisorctl start b402-gunicorn')
def mac_setup_bdist_mpkg():
with cd(mac_tmp):
run("git clone https://github.com/rgommers/bdist_mpkg.git")
with cd("bdist_mpkg"):
with prefix(mac_prefix):
run("python setup.py install --prefix=../usr")
def init_biostar():
with prefix(env.workon):
run("./biostar.sh index")
def pull():
"""Perform a pull on remote"""
with prefix(env.workon):
run("git pull")
def _init_virtualenv():
"""Creates initial virtualenv"""
run('virtualenv -p %(python)s --no-site-packages %(env_path)s' % env)
with prefix('source %(env_path)s/bin/activate' % env):
run('easy_install pip')
def _update_requirements():
"""Updates dependencies defined in the requirements file"""
with prefix('source %(env_path)s/bin/activate' % env):
run('pip install -U -r %(project_repo_path)s/requirements.pip' % env)
run('chmod -R go=u,go-w %(env_path)s' % env)
def syncdb():
"""Runs `syncdb` to create the DB schema"""
require('environment', provided_by=[ubuntu, fedora])
with cd('%(project_repo_path)s' % env):
with prefix('source %(env_path)s/bin/activate' % env):
run('python manage.py syncdb')
def install_protkgem(env):
"""This method installs Ira Cooke's ProtK framework for the galaxy user.
By default this will install ProtK from rubygems server, but if
env.protk_version is set to <version>@<url> (e.g.
1.1.5@https://bitbucket.org/iracooke/protk-working) the
gem will be cloned with hg and installed from source.
"""
_prep_galaxy(env)
default_version = "1.2.0"
version_and_revision = env.get("protk_version", default_version)
install_from_source = version_and_revision.find("@") > 0
# e.g. protk_version = 1.1.5@https://bitbucket.org/iracooke/protk-working
if install_from_source:
(version, revision) = version_and_revision.split("@")
url = _get_bitbucket_download_url(
revision, "https://bitbucket.org/iracooke/protk")
else:
version = version_and_revision
ruby_version = "1.9.3"
force_rvm_install = False
with prefix("HOME=~%s" % env.galaxy_user):
def rvm_exec(env, cmd="", rvm_cmd="use"):
prefix = ". $HOME/.rvm/scripts/rvm; rvm %s %s; " % (rvm_cmd,
ruby_version)
env.safe_sudo("%s %s" % (prefix, cmd), user=env.galaxy_user)
if not exists("$HOME/.rvm") or force_rvm_install:
env.safe_sudo(
"curl -L get.rvm.io | bash -s stable; source ~%s/.rvm/scripts/rvm"
% (env.galaxy_user),
user=env.galaxy_user)
rvm_exec(env, rvm_cmd="install")
if not install_from_source:
# Typical rubygem install
rvm_exec(env,
"gem install --no-ri --no-rdoc protk -v %s" % version)
else:
with cd("~%s" % env.galaxy_user):
env.safe_sudo(
"rm -rf protk_source; hg clone '%s' protk_source" % url,
user=env.galaxy_user)
rvm_exec(
env,
"cd protk_source; gem build protk.gemspec; gem install protk"
)
protk_properties = {}
## ProtK can set these up itself, should make that an option.
protk_properties["tpp_root"] = os.path.join(env.galaxy_tools_dir,
"transproteomic_pipeline",
"default")
protk_properties[
'openms_root'] = "/usr" # os.path.join(env.galaxy_tools_dir, "openms", "default", "bin")
### Assumes omssa, blast, and transproteomic_pipeline CBL galaxy installs.
protk_properties['omssa_root'] = os.path.join(env.galaxy_tools_dir,
"omssa", "default",
"bin")
protk_properties['blast_root'] = os.path.join(env.galaxy_tools_dir,
"blast+", "default")
protk_properties['pwiz_root'] = os.path.join(
env.galaxy_tools_dir, "transproteomic_pipeline", "default", "bin")
# Other properties: log_file, blast_root
env.safe_sudo("mkdir -p \"$HOME/.protk\"", user=env.galaxy_user)
env.safe_sudo("mkdir -p \"$HOME/.protk/Databases\"",
user=env.galaxy_user)
_write_to_file(yaml.dump(protk_properties),
"/home/%s/.protk/config.yml" % env.galaxy_user, 0755)
rvm_exec(env, "protk_setup.rb galaxyenv")
install_dir = os.path.join(env.galaxy_tools_dir, "protkgem", version)
env.safe_sudo("mkdir -p '%s'" % install_dir)
_chown_galaxy(env, install_dir)
env.safe_sudo('ln -s -f "$HOME/.protk/galaxy/env.sh" "%s/env.sh"' %
install_dir,
user=env.galaxy_user)
with cd(install_dir):
with cd(".."):
env.safe_sudo("ln -s -f '%s' default" % version)
def run_python(*args, **kwargs):
activate_virtual_env = \
"source {venv}/bin/activate".format(
venv=env.py_virtual_env)
with prefix(activate_virtual_env):
run(*args, **kwargs)
def run_in_ve(command):
"""Execute the command inside the virtualenv."""
with prefix('. %s' % env.activate_path):
env.doit(command)
def migrate():
"""Migrate from main"""
with prefix(env.workon):
run("python manage.py migrate")
def virtualenv():
with cd(env.proj_root):
with prefix('source venv/bin/activate'):
yield
def index():
"""Index the content"""
with prefix(env.workon):
run("./biostar.sh index")
def install_package(package_name, active_file_path, version):
with prefix('source {}'.format(active_file_path)):
pip('typeidea', version)
def pyenv_env(version):
cmd_dir = os.path.join(env.pyenv_dir, 'versions',
'indico-build-{0}'.format(version), 'bin')
with prefix('PATH={0}:$PATH'.format(cmd_dir)):
yield
def test():
"""Run test"""
with prefix(env.workon):
run("./biostar.sh test")
def pip():
"""Reinstall requirments"""
with prefix(env.workon):
run("pip install -r conf/requirements/base.txt")
def collect_static():
with prefix('source ' + ACTIVATE_SCRIPT):
run(PYTHON_EXECUTABLE + ' manage.py collectstatic --no-input')
def virtualenv():
with cd(env.DJANGO_PATH):
activate = "source %s" % env.VIRTUALENV_ACTIVATE
with prefix(activate):
yield
def freeze_results(*args):
with cd(env.project_path):
with prefix('workon %s' % env.virtualenv_name):
run('python manage.py freeze_results ' + ' '.join(args))
def compile_translations():
with prefix('workon %s' % env.virtualenv_name):
with cd(env.project_path):
run('cd trojsten && python ../manage.py compilemessages')
def install_requirements(environment):
if environment == "local":
with cd("/vagrant/"):
with prefix("source /home/vagrant/envs/{0}/bin/activate".format(env.project_name)):
run("pip install -r requirements.txt")
def migrate():
with prefix('source ' + ACTIVATE_SCRIPT):
run(PYTHON_EXECUTABLE + ' manage.py migrate')
def run_command(name, argv):
args = " ".join(argv[1:])
with cd("~/working/%s" % (name)):
with prefix("source setupenv.sh"):
run("%s" % (args))
def virtualenv():
if hasattr(env, 'virtualenv'):
with prefix('source {virtualenv}/bin/activate'.format(**env)):
yield
else:
yield
def virtualenv(virt=config.virtualenv_name):
with cd(env.path):
with prefix("source {}/virt/{}/bin/activate".format(env.path, virt)):
yield
def manage(*args):
with cd(env.project_path):
with prefix('workon %s' % env.virtualenv_name):
run('python manage.py ' + ' '.join(args))
